From a5e9505e9c52bcc38ad14b665937d76cc40d0ece Mon Sep 17 00:00:00 2001
From: Daniel Turek <danielturek@gmail.com>
Date: Thu, 27 Jun 2024 20:27:22 -0400
Subject: [PATCH] rebuilt package

---
 nimbleHMC/man/addHMC.Rd               | 13 ++++++++-----
 nimbleHMC/man/sampler_NUTS.Rd         |  9 ++++++---
 nimbleHMC/man/sampler_NUTS_classic.Rd |  9 ++++++---
 3 files changed, 20 insertions(+), 11 deletions(-)

diff --git a/nimbleHMC/man/addHMC.Rd b/nimbleHMC/man/addHMC.Rd
index a77fdd4..c288c7d 100644
--- a/nimbleHMC/man/addHMC.Rd
+++ b/nimbleHMC/man/addHMC.Rd
@@ -17,7 +17,7 @@ addHMC(
 \arguments{
 \item{conf}{A nimble MCMC configuration object, as returned by `configureMCMC`.}
 
-\item{target}{A character vector of continuous-valued stochastic node names to sample.  If this argument contains any discrete-valued nodes, an error is produced and no sampler is added.}
+\item{target}{A character vector of continuous-valued stochastic node names to sample.  If this argument contains any discrete-valued nodes, an error is produced and no HMC sampler is added.  If this argument is omitted, then no HMC sampler is added.}
 
 \item{type}{A character string specifying the type of HMC sampler to add, either "NUTS" or "NUTS_classic".  See `help(NUTS)` or `help(NUTS_classic)` for details of each sampler.  The default sampler type is "NUTS".}
 
@@ -60,11 +60,14 @@ inits <- list(b0 = 1, b1 = 0.1, sigma = 1)
 
 Rmodel <- nimbleModel(code, constants, data, inits, buildDerivs = TRUE)
 
-## create MCMC configuration object
-conf <- configureMCMC(Rmodel, nodes = NULL)
+## create default MCMC configuration object
+conf <- configureMCMC(Rmodel)
 
-## add HMC sampler operating on all stochastic model nodes
-addHMC(conf)
+## remove default samplers operating on b0 and b1
+conf$removeSamplers(c("b0", "b1"))
+
+## add an HMC sampler operating on b0 and b1
+addHMC(conf, target = c("b0", "b1"))
 
 Rmcmc <- buildMCMC(conf)
 
diff --git a/nimbleHMC/man/sampler_NUTS.Rd b/nimbleHMC/man/sampler_NUTS.Rd
index 39b7c9b..1a82e1c 100644
--- a/nimbleHMC/man/sampler_NUTS.Rd
+++ b/nimbleHMC/man/sampler_NUTS.Rd
@@ -63,9 +63,12 @@ code <- nimbleCode({
     }
 })
 
-N <- 10
-constants <- list(N = N, x = 1:N)
-data <- list(y = 1:N)
+set.seed(0)
+N <- 100
+x <- rnorm(N)
+y <- 1 + 0.3*x + rnorm(N)
+constants <- list(N = N, x = x)
+data <- list(y = y)
 inits <- list(b0 = 1, b1 = 0.1, sigma = 1)
 
 Rmodel <- nimbleModel(code, constants, data, inits, buildDerivs = TRUE)
diff --git a/nimbleHMC/man/sampler_NUTS_classic.Rd b/nimbleHMC/man/sampler_NUTS_classic.Rd
index 17e720d..faa1200 100644
--- a/nimbleHMC/man/sampler_NUTS_classic.Rd
+++ b/nimbleHMC/man/sampler_NUTS_classic.Rd
@@ -63,9 +63,12 @@ code <- nimbleCode({
     }
 })
 
-N <- 10
-constants <- list(N = N, x = 1:N)
-data <- list(y = 1:N)
+set.seed(0)
+N <- 100
+x <- rnorm(N)
+y <- 1 + 0.3*x + rnorm(N)
+constants <- list(N = N, x = x)
+data <- list(y = y)
 inits <- list(b0 = 1, b1 = 0.1, sigma = 1)
 
 Rmodel <- nimbleModel(code, constants, data, inits, buildDerivs = TRUE)